Constructing Synthetic Microbial Communities to Explore the Ecology and Evolution of Symbiosis

2014 ◽  
pp. 27-38 ◽  
Author(s):  
Adam James Waite ◽  
Wenying Shou
Keyword(s):  
Microbial Communities ◽  
Evolution Of Symbiosis ◽  
Synthetic Microbial Communities

A peek in the micro-sized world: a review of design principles, engineering tools, and applications of engineered microbial community

2020 ◽  
Vol 48 (2) ◽  
pp. 399-409
Author(s):  
Baizhen Gao ◽  
Rushant Sabnis ◽  
Tommaso Costantini ◽  
Robert Jinkerson ◽  
Qing Sun
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Environmental Remediation ◽  
Real Life ◽  
Design Principles ◽  
Microbial Interactions ◽  
Potential Applications ◽  
New Gene ◽  
Global Biogeochemical Cycles ◽  
Synthetic Microbial Communities

Microbial communities drive diverse processes that impact nearly everything on this planet, from global biogeochemical cycles to human health. Harnessing the power of these microorganisms could provide solutions to many of the challenges that face society. However, naturally occurring microbial communities are not optimized for anthropogenic use. An emerging area of research is focusing on engineering synthetic microbial communities to carry out predefined functions. Microbial community engineers are applying design principles like top-down and bottom-up approaches to create synthetic microbial communities having a myriad of real-life applications in health care, disease prevention, and environmental remediation. Multiple genetic engineering tools and delivery approaches can be used to ‘knock-in' new gene functions into microbial communities. A systematic study of the microbial interactions, community assembling principles, and engineering tools are necessary for us to understand the microbial community and to better utilize them. Continued analysis and effort are required to further the current and potential applications of synthetic microbial communities.

scholarly journals Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Cristal Zuñiga ◽  
Tingting Li ◽  
Michael T. Guarnieri ◽  
Jackson P. Jenkins ◽  
Chien-Ting Li ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Sustainable Growth ◽  
Synthetic Microbial Communities

scholarly journals Massively parallel screening of synthetic microbial communities

2019 ◽  
Vol 116 (26) ◽  
pp. 12804-12809 ◽  
Author(s):  
Jared Kehe ◽  
Anthony Kulesa ◽  
Anthony Ortiz ◽  
Cheri M. Ackerman ◽  
Sri Gowtham Thakku ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Massively Parallel ◽  
Phenotypic Characterization ◽  
Interspecies Interactions ◽  
Additional Species ◽  
Plant Symbiont ◽  
Complementary Approach ◽  
Potential Applications ◽  
Synthetic Microbial Communities

Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiontHerbaspirillum frisingensein a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.

High‐resolution phenotyping of sorghum genotypic and phenotypic responses to low nitrogen and synthetic microbial communities

2021 ◽  
Author(s):  
Yen Ning Chai ◽  
Yufeng Ge ◽  
Vincent Stoerger ◽  
Daniel P. Schachtman
Keyword(s):  
High Resolution ◽  
Microbial Communities ◽  
Synthetic Microbial Communities ◽  
Low Nitrogen ◽  
Phenotypic Responses

scholarly journals Rbec: a tool for analysis of amplicon sequencing data from synthetic microbial communities

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Pengfan Zhang ◽  
Stjin Spaepen ◽  
Yang Bai ◽  
Stephane Hacquard ◽  
Ruben Garrido-Oter
Keyword(s):  
Microbial Communities ◽  
Amplicon Sequencing ◽  
Fungal Communities ◽  
Polymorphic Variation ◽  
Sequencing Data ◽  
Sequencing Errors ◽  
Extensive Evaluation ◽  
Culture Independent ◽  
Reference Sequences ◽  
Synthetic Microbial Communities

AbstractSynthetic microbial communities (SynComs) constitute an emerging and powerful tool in biological, biomedical, and biotechnological research. Despite recent advances in algorithms for the analysis of culture-independent amplicon sequencing data from microbial communities, there is a lack of tools specifically designed for analyzing SynCom data, where reference sequences for each strain are available. Here we present Rbec, a tool designed for the analysis of SynCom data that accurately corrects PCR and sequencing errors in amplicon sequences and identifies intra-strain polymorphic variation. Extensive evaluation using mock bacterial and fungal communities show that our tool outperforms current methods for samples of varying complexity, diversity, and sequencing depth. Furthermore, Rbec also allows accurate detection of contaminants in SynCom experiments.

scholarly journals Metabolic Modelling Approaches for Describing and Engineering Microbial Communities

2020 ◽  
Author(s):  
Beatriz García-Jiménez ◽  
Jesús Torres ◽  
Juan Nogales
Keyword(s):  
Microbial Communities ◽  
Microbial Consortia ◽  
Huge Number ◽  
Metabolic Modelling ◽  
Rational Engineering ◽  
Wet Lab ◽  
Synthetic Microbial Communities ◽  
Advance Knowledge ◽  
Natural And Synthetic

Microbes do not live in isolation but in microbial communities. The relevance of microbial communities is increasing due to the awareness about their biotechnological influences in a huge number of environmental, health and industrial processes. Hence, being able to control and engineer the output of both natural and synthetic communities would be of great interest. However, most of the available methods and biotechnological applications (both in vivo and in silico) have been developed in the context of isolated microbes. In vivo microbial consortia development, i.e. to reproduce the community life conditions in the wet-lab, is extremely difficult and expensive requiring of computational approaches to advance knowledge about microbial communities, mainly with descriptive modelling, and further with engineering modelling. In this review we provide a detailed compilation of available examples of engineered microbial communities as a launch pad for an exhaustive and historical revision of those computational methods devoted so far toward the better understanding, and rational engineering of natural and synthetic microbial communities.

scholarly journals Complex function by design using spatially pre-structured synthetic microbial communities: degradation of pentachlorophenol in the presence of Hg(ii)

2011 ◽  
Vol 3 (2) ◽  
pp. 126-133 ◽  
Author(s):  
Hyun Jung Kim ◽  
Wenbin Du ◽  
Rustem F. Ismagilov
Keyword(s):  
Microbial Communities ◽  
Complex Function ◽  
Synthetic Microbial Communities
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